Multiple sequence alignment - TraesCS7B01G008800

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7B01G008800 chr7B 100.000 4934 0 0 1 4934 5281366 5286299 0.000000e+00 9112.0
1 TraesCS7B01G008800 chr7B 87.462 3326 360 34 772 4088 5503193 5506470 0.000000e+00 3779.0
2 TraesCS7B01G008800 chr7B 88.347 2154 230 14 1937 4088 5338212 5340346 0.000000e+00 2567.0
3 TraesCS7B01G008800 chr7B 82.888 1496 222 27 367 1846 5336683 5338160 0.000000e+00 1314.0
4 TraesCS7B01G008800 chr7B 85.913 1008 98 18 266 1249 5317489 5318476 0.000000e+00 1035.0
5 TraesCS7B01G008800 chr7B 86.266 466 36 10 269 720 5502743 5503194 9.610000e-132 481.0
6 TraesCS7B01G008800 chr7B 89.434 265 17 6 1 263 5317179 5317434 1.710000e-84 324.0
7 TraesCS7B01G008800 chr7B 91.150 113 8 2 4475 4585 5219931 5220043 8.550000e-33 152.0
8 TraesCS7B01G008800 chr7B 84.173 139 17 4 1 134 5215780 5215918 4.010000e-26 130.0
9 TraesCS7B01G008800 chr7B 83.916 143 16 4 1 137 5509373 5509514 4.010000e-26 130.0
10 TraesCS7B01G008800 chr7B 97.436 39 0 1 266 304 5317558 5317595 1.150000e-06 65.8
11 TraesCS7B01G008800 chr7B 94.737 38 0 1 269 304 5502810 5502847 1.920000e-04 58.4
12 TraesCS7B01G008800 chr7B 92.308 39 1 2 342 378 5281631 5281669 2.000000e-03 54.7
13 TraesCS7B01G008800 chr7D 88.118 3863 366 45 266 4090 64265294 64269101 0.000000e+00 4505.0
14 TraesCS7B01G008800 chr7D 86.484 3751 424 51 367 4088 64245020 64248716 0.000000e+00 4041.0
15 TraesCS7B01G008800 chr7D 84.977 3954 493 62 335 4231 63944182 63940273 0.000000e+00 3917.0
16 TraesCS7B01G008800 chr7D 87.386 2418 286 15 639 3044 64222705 64225115 0.000000e+00 2758.0
17 TraesCS7B01G008800 chr7D 88.776 2165 228 11 1744 3904 59938408 59936255 0.000000e+00 2638.0
18 TraesCS7B01G008800 chr7D 85.031 1276 165 14 462 1719 59939860 59938593 0.000000e+00 1275.0
19 TraesCS7B01G008800 chr7D 86.099 223 19 5 45 263 64265025 64265239 3.840000e-56 230.0
20 TraesCS7B01G008800 chr7D 86.232 138 15 3 1 134 64244652 64244789 3.980000e-31 147.0
21 TraesCS7B01G008800 chr7D 83.571 140 11 5 4800 4934 59934984 59934852 2.410000e-23 121.0
22 TraesCS7B01G008800 chr7D 97.436 39 0 1 266 304 64265363 64265400 1.150000e-06 65.8
23 TraesCS7B01G008800 chr7A 90.268 3134 298 5 773 3902 68029181 68032311 0.000000e+00 4091.0
24 TraesCS7B01G008800 chr7A 85.702 3595 436 52 750 4315 67985109 67988654 0.000000e+00 3720.0
25 TraesCS7B01G008800 chr7A 84.618 3335 444 38 773 4088 68043133 68046417 0.000000e+00 3253.0
26 TraesCS7B01G008800 chr7A 87.078 2221 243 29 266 2464 67593491 67591293 0.000000e+00 2471.0
27 TraesCS7B01G008800 chr7A 86.679 2207 252 19 1886 4088 68083599 68085767 0.000000e+00 2409.0
28 TraesCS7B01G008800 chr7A 86.222 1350 158 13 328 1659 68076647 68077986 0.000000e+00 1437.0
29 TraesCS7B01G008800 chr7A 89.700 466 32 7 266 725 67984662 67985117 9.210000e-162 580.0
30 TraesCS7B01G008800 chr7A 84.490 245 16 11 30 261 67984368 67984603 6.430000e-54 222.0
31 TraesCS7B01G008800 chr7A 84.082 245 17 11 30 261 67593785 67593550 2.990000e-52 217.0
32 TraesCS7B01G008800 chr7A 85.714 84 8 3 55 134 68076334 68076417 8.800000e-13 86.1
33 TraesCS7B01G008800 chr7A 94.872 39 0 2 266 304 67593419 67593383 5.330000e-05 60.2
34 TraesCS7B01G008800 chr2A 91.551 722 45 8 3720 4437 719082488 719083197 0.000000e+00 981.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7B01G008800 chr7B 5281366 5286299 4933 False 9112.000000 9112 100.000000 1 4934 1 chr7B.!!$F3 4933
1 TraesCS7B01G008800 chr7B 5336683 5340346 3663 False 1940.500000 2567 85.617500 367 4088 2 chr7B.!!$F6 3721
2 TraesCS7B01G008800 chr7B 5502743 5509514 6771 False 1112.100000 3779 88.095250 1 4088 4 chr7B.!!$F7 4087
3 TraesCS7B01G008800 chr7B 5317179 5318476 1297 False 474.933333 1035 90.927667 1 1249 3 chr7B.!!$F5 1248
4 TraesCS7B01G008800 chr7D 63940273 63944182 3909 True 3917.000000 3917 84.977000 335 4231 1 chr7D.!!$R1 3896
5 TraesCS7B01G008800 chr7D 64222705 64225115 2410 False 2758.000000 2758 87.386000 639 3044 1 chr7D.!!$F1 2405
6 TraesCS7B01G008800 chr7D 64244652 64248716 4064 False 2094.000000 4041 86.358000 1 4088 2 chr7D.!!$F2 4087
7 TraesCS7B01G008800 chr7D 64265025 64269101 4076 False 1600.266667 4505 90.551000 45 4090 3 chr7D.!!$F3 4045
8 TraesCS7B01G008800 chr7D 59934852 59939860 5008 True 1344.666667 2638 85.792667 462 4934 3 chr7D.!!$R2 4472
9 TraesCS7B01G008800 chr7A 68029181 68032311 3130 False 4091.000000 4091 90.268000 773 3902 1 chr7A.!!$F1 3129
10 TraesCS7B01G008800 chr7A 68043133 68046417 3284 False 3253.000000 3253 84.618000 773 4088 1 chr7A.!!$F2 3315
11 TraesCS7B01G008800 chr7A 68083599 68085767 2168 False 2409.000000 2409 86.679000 1886 4088 1 chr7A.!!$F3 2202
12 TraesCS7B01G008800 chr7A 67984368 67988654 4286 False 1507.333333 3720 86.630667 30 4315 3 chr7A.!!$F4 4285
13 TraesCS7B01G008800 chr7A 67591293 67593785 2492 True 916.066667 2471 88.677333 30 2464 3 chr7A.!!$R1 2434
14 TraesCS7B01G008800 chr7A 68076334 68077986 1652 False 761.550000 1437 85.968000 55 1659 2 chr7A.!!$F5 1604
15 TraesCS7B01G008800 chr2A 719082488 719083197 709 False 981.000000 981 91.551000 3720 4437 1 chr2A.!!$F1 717

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
256 361 0.394192 TGGTCAGTGGTCAGAGCTTG 59.606 55.000 0.38 0.13 33.63 4.01 F
1064 1273 0.662619 TCAAGCAGCAAACCAACGAG 59.337 50.000 0.00 0.00 0.00 4.18 F
1070 1279 1.001487 CAGCAAACCAACGAGCATGAA 60.001 47.619 0.00 0.00 0.00 2.57 F
2355 2762 1.375523 GGGCCGTGGAGTTACACAG 60.376 63.158 0.00 0.00 41.38 3.66 F
3376 3789 1.268896 GCAGATTGAATGACCGCATGG 60.269 52.381 0.00 0.00 42.84 3.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2601 0.899720 ACTACCCGCAAATCTTCCGA 59.100 50.000 0.00 0.0 0.0 4.55 R
2333 2740 1.195442 TGTAACTCCACGGCCCATCA 61.195 55.000 0.00 0.0 0.0 3.07 R
2604 3011 2.173519 ACCGTTCCTTCCTCGTTGATA 58.826 47.619 0.00 0.0 0.0 2.15 R
3553 3969 0.108585 AGAAACCGAAGAGCAGGCAA 59.891 50.000 0.00 0.0 0.0 4.52 R
4802 6381 0.393448 GAAGAGGGGCCTCGGAATAC 59.607 60.000 0.84 0.0 46.9 1.89 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 1.806247 GCCACAGGTTCAACTTTTGCC 60.806 52.381 0.00 0.00 0.00 4.52
256 361 0.394192 TGGTCAGTGGTCAGAGCTTG 59.606 55.000 0.38 0.13 33.63 4.01
263 370 2.499289 AGTGGTCAGAGCTTGGTATCTG 59.501 50.000 0.38 0.00 43.53 2.90
269 376 5.227569 TCAGAGCTTGGTATCTGAAAACA 57.772 39.130 2.54 0.00 46.74 2.83
270 377 5.620206 TCAGAGCTTGGTATCTGAAAACAA 58.380 37.500 2.54 0.00 46.74 2.83
271 378 6.061441 TCAGAGCTTGGTATCTGAAAACAAA 58.939 36.000 2.54 0.00 46.74 2.83
272 379 6.716628 TCAGAGCTTGGTATCTGAAAACAAAT 59.283 34.615 2.54 0.00 46.74 2.32
273 380 7.882791 TCAGAGCTTGGTATCTGAAAACAAATA 59.117 33.333 2.54 0.00 46.74 1.40
274 381 8.514594 CAGAGCTTGGTATCTGAAAACAAATAA 58.485 33.333 0.00 0.00 44.68 1.40
276 383 9.508567 GAGCTTGGTATCTGAAAACAAATAATC 57.491 33.333 0.00 0.00 0.00 1.75
277 384 9.023962 AGCTTGGTATCTGAAAACAAATAATCA 57.976 29.630 0.00 0.00 0.00 2.57
286 393 8.963725 TCTGAAAACAAATAATCAGATCATGCT 58.036 29.630 0.00 0.00 42.36 3.79
291 398 8.937634 AACAAATAATCAGATCATGCTTTTCC 57.062 30.769 0.00 0.00 0.00 3.13
292 399 8.070034 ACAAATAATCAGATCATGCTTTTCCA 57.930 30.769 0.00 0.00 0.00 3.53
293 400 8.533657 ACAAATAATCAGATCATGCTTTTCCAA 58.466 29.630 0.00 0.00 0.00 3.53
294 401 9.373603 CAAATAATCAGATCATGCTTTTCCAAA 57.626 29.630 0.00 0.00 0.00 3.28
295 402 8.937634 AATAATCAGATCATGCTTTTCCAAAC 57.062 30.769 0.00 0.00 0.00 2.93
296 403 5.988310 ATCAGATCATGCTTTTCCAAACA 57.012 34.783 0.00 0.00 0.00 2.83
297 404 5.787953 TCAGATCATGCTTTTCCAAACAA 57.212 34.783 0.00 0.00 0.00 2.83
298 405 6.159299 TCAGATCATGCTTTTCCAAACAAA 57.841 33.333 0.00 0.00 0.00 2.83
301 408 8.366401 TCAGATCATGCTTTTCCAAACAAATTA 58.634 29.630 0.00 0.00 0.00 1.40
302 409 8.653338 CAGATCATGCTTTTCCAAACAAATTAG 58.347 33.333 0.00 0.00 0.00 1.73
303 410 8.370182 AGATCATGCTTTTCCAAACAAATTAGT 58.630 29.630 0.00 0.00 0.00 2.24
304 411 7.712264 TCATGCTTTTCCAAACAAATTAGTG 57.288 32.000 0.00 0.00 0.00 2.74
305 412 6.705381 TCATGCTTTTCCAAACAAATTAGTGG 59.295 34.615 0.00 0.00 0.00 4.00
306 413 6.227298 TGCTTTTCCAAACAAATTAGTGGA 57.773 33.333 0.00 0.00 38.39 4.02
307 414 6.279882 TGCTTTTCCAAACAAATTAGTGGAG 58.720 36.000 0.00 0.00 41.10 3.86
309 416 7.068839 TGCTTTTCCAAACAAATTAGTGGAGTA 59.931 33.333 0.00 0.00 41.10 2.59
312 419 8.934023 TTTCCAAACAAATTAGTGGAGTATCT 57.066 30.769 0.00 0.00 41.10 1.98
313 420 7.921786 TCCAAACAAATTAGTGGAGTATCTG 57.078 36.000 0.00 0.00 35.22 2.90
314 421 7.685481 TCCAAACAAATTAGTGGAGTATCTGA 58.315 34.615 0.00 0.00 35.22 3.27
315 422 8.160765 TCCAAACAAATTAGTGGAGTATCTGAA 58.839 33.333 0.00 0.00 35.22 3.02
316 423 8.792633 CCAAACAAATTAGTGGAGTATCTGAAA 58.207 33.333 0.00 0.00 32.54 2.69
319 426 8.918202 ACAAATTAGTGGAGTATCTGAAAACA 57.082 30.769 0.00 0.00 33.73 2.83
320 427 9.349713 ACAAATTAGTGGAGTATCTGAAAACAA 57.650 29.630 0.00 0.00 33.73 2.83
322 429 9.574516 AAATTAGTGGAGTATCTGAAAACAACT 57.425 29.630 0.00 0.00 33.73 3.16
324 431 9.877178 ATTAGTGGAGTATCTGAAAACAACTAG 57.123 33.333 0.00 0.00 33.73 2.57
325 432 7.304497 AGTGGAGTATCTGAAAACAACTAGT 57.696 36.000 0.00 0.00 33.73 2.57
327 434 9.036980 AGTGGAGTATCTGAAAACAACTAGTAT 57.963 33.333 0.00 0.00 33.73 2.12
328 435 9.088512 GTGGAGTATCTGAAAACAACTAGTATG 57.911 37.037 0.00 0.00 33.73 2.39
329 436 7.764443 TGGAGTATCTGAAAACAACTAGTATGC 59.236 37.037 0.00 0.00 33.73 3.14
332 439 4.250464 TCTGAAAACAACTAGTATGCCCG 58.750 43.478 0.00 0.00 0.00 6.13
334 441 3.244630 TGAAAACAACTAGTATGCCCGGT 60.245 43.478 0.00 0.00 0.00 5.28
336 443 3.428413 AACAACTAGTATGCCCGGTTT 57.572 42.857 0.00 0.00 0.00 3.27
337 444 3.428413 ACAACTAGTATGCCCGGTTTT 57.572 42.857 0.00 0.00 0.00 2.43
349 510 2.096174 GCCCGGTTTTTCCAAACAAAAC 59.904 45.455 0.00 0.53 43.76 2.43
413 574 6.252655 GCTGTTACTTTCACGAAACACAAATT 59.747 34.615 0.00 0.00 0.00 1.82
444 605 1.524863 CTCGTCCGGTGGTTCTCTGT 61.525 60.000 0.00 0.00 0.00 3.41
456 619 5.695363 GGTGGTTCTCTGTAAACAGTTAGTC 59.305 44.000 9.81 0.74 44.12 2.59
470 636 5.417580 AACAGTTAGTCTGGTTTTTGCTGAA 59.582 36.000 0.00 0.00 42.00 3.02
473 639 3.904136 AGTCTGGTTTTTGCTGAATCG 57.096 42.857 0.00 0.00 0.00 3.34
581 777 4.783227 TGCTATTCAAGGTACCCTTCTTCT 59.217 41.667 8.74 0.00 42.67 2.85
582 778 5.119694 GCTATTCAAGGTACCCTTCTTCTG 58.880 45.833 8.74 0.00 42.67 3.02
631 833 3.786657 TGCATATGCGCTATGTTTACG 57.213 42.857 22.21 0.00 45.83 3.18
692 894 9.185192 CTCATTCTGTCTTTTGAAAACCATTAC 57.815 33.333 0.00 0.00 0.00 1.89
742 944 5.366768 AGGACAATGCTATAGTGGTGTGTAT 59.633 40.000 0.84 0.00 0.00 2.29
743 945 5.696724 GGACAATGCTATAGTGGTGTGTATC 59.303 44.000 0.84 0.00 0.00 2.24
744 946 6.233905 ACAATGCTATAGTGGTGTGTATCA 57.766 37.500 0.84 0.00 0.00 2.15
755 960 4.036262 GTGGTGTGTATCAAGTGCAAAGAA 59.964 41.667 0.00 0.00 0.00 2.52
759 964 6.701400 GGTGTGTATCAAGTGCAAAGAAAAAT 59.299 34.615 0.00 0.00 0.00 1.82
834 1043 3.188011 CTCGGTGAGCTGCTCGTA 58.812 61.111 23.35 5.37 32.35 3.43
879 1088 4.032558 CGAGTAAAGAAAGGCGTACAATCC 59.967 45.833 0.00 0.00 0.00 3.01
888 1097 1.537562 GGCGTACAATCCCTCCTTACG 60.538 57.143 0.00 0.00 38.80 3.18
968 1177 2.008268 GACGAGCCGGTCCGGATTTA 62.008 60.000 34.84 0.00 45.97 1.40
1056 1265 1.888512 GATGAGGGTTCAAGCAGCAAA 59.111 47.619 0.00 0.00 36.78 3.68
1064 1273 0.662619 TCAAGCAGCAAACCAACGAG 59.337 50.000 0.00 0.00 0.00 4.18
1070 1279 1.001487 CAGCAAACCAACGAGCATGAA 60.001 47.619 0.00 0.00 0.00 2.57
1160 1369 4.025040 TCTGTGATGCCATTGAAGAAGT 57.975 40.909 0.00 0.00 0.00 3.01
1232 1441 4.243270 GACATGTTTAGCTCTACCAACGT 58.757 43.478 0.00 0.00 0.00 3.99
1343 1552 5.104259 ACACTTATTTCTGAGGATGGGAC 57.896 43.478 0.00 0.00 0.00 4.46
1351 1560 4.609866 TCTGAGGATGGGACTTCTAAGA 57.390 45.455 0.00 0.00 0.00 2.10
1364 1573 6.431234 GGGACTTCTAAGAAGCAATTGAAGAA 59.569 38.462 10.34 6.62 36.00 2.52
1473 1682 2.026905 GCTTTTGTCCCAGTGGGTCAA 61.027 52.381 30.02 30.02 45.99 3.18
1476 1685 2.765689 TTGTCCCAGTGGGTCAAAAT 57.234 45.000 31.11 0.00 45.05 1.82
1492 1701 6.607198 GGGTCAAAATCCAGATATCAGGAAAA 59.393 38.462 19.61 0.00 35.11 2.29
1493 1702 7.124147 GGGTCAAAATCCAGATATCAGGAAAAA 59.876 37.037 19.61 0.00 35.11 1.94
1525 1734 2.674796 ACTCTATGGCCTCGACAAAC 57.325 50.000 3.32 0.00 0.00 2.93
1854 2238 8.685427 ACATTTTTGCATGCATATAGTTAGTGA 58.315 29.630 23.37 0.00 0.00 3.41
1855 2239 8.961092 CATTTTTGCATGCATATAGTTAGTGAC 58.039 33.333 23.37 0.00 0.00 3.67
1888 2290 4.935808 CCTGTGGTTTGCTTAGTACCTTAG 59.064 45.833 0.00 0.00 33.05 2.18
1896 2299 9.833917 GGTTTGCTTAGTACCTTAGAATTATCT 57.166 33.333 0.00 0.00 39.82 1.98
1938 2344 9.855021 GTTGTATATAATTTGACTTGCCAACTT 57.145 29.630 0.00 0.00 0.00 2.66
1946 2353 7.944729 ATTTGACTTGCCAACTTATGATACT 57.055 32.000 0.00 0.00 0.00 2.12
2028 2435 6.198966 GGAGATTTATAAATTGCGCTTTGTGG 59.801 38.462 9.73 0.00 0.00 4.17
2194 2601 5.712152 ATTTCAAAGCGAGGAGAAATGTT 57.288 34.783 0.00 0.00 38.76 2.71
2196 2603 2.736721 TCAAAGCGAGGAGAAATGTTCG 59.263 45.455 0.00 0.00 36.23 3.95
2219 2626 3.366440 AGATTTGCGGGTAGTATCGAC 57.634 47.619 0.00 0.00 0.00 4.20
2221 2628 3.131577 AGATTTGCGGGTAGTATCGACAA 59.868 43.478 0.00 0.00 0.00 3.18
2274 2681 7.826252 CCATTAGCCATCATTACAATAGCTAGT 59.174 37.037 0.00 0.00 33.31 2.57
2287 2694 5.361285 ACAATAGCTAGTCTCCTGGTTAGTG 59.639 44.000 0.00 0.00 37.12 2.74
2355 2762 1.375523 GGGCCGTGGAGTTACACAG 60.376 63.158 0.00 0.00 41.38 3.66
2415 2822 5.163269 ACTCAGCTATTATGACTTGCCATCA 60.163 40.000 0.00 0.00 0.00 3.07
2427 2834 3.890756 ACTTGCCATCACATTTGAAGACA 59.109 39.130 0.00 0.00 34.61 3.41
2471 2878 6.595682 TCTTTCCTGAAGACTTTGAGATTGT 58.404 36.000 0.00 0.00 39.44 2.71
2474 2881 5.928976 TCCTGAAGACTTTGAGATTGTGAA 58.071 37.500 0.00 0.00 0.00 3.18
2592 2999 4.853007 AGCTTATGAACAGGAGCTTGATT 58.147 39.130 8.27 0.00 42.46 2.57
2604 3011 2.165845 GAGCTTGATTCAGCCAGCAAAT 59.834 45.455 10.58 0.00 41.12 2.32
2626 3033 1.962807 TCAACGAGGAAGGAACGGTAA 59.037 47.619 0.00 0.00 0.00 2.85
2627 3034 2.064014 CAACGAGGAAGGAACGGTAAC 58.936 52.381 0.00 0.00 0.00 2.50
2674 3081 3.248602 GCTTGACCTTATATGCTCGTTGG 59.751 47.826 0.00 0.00 0.00 3.77
2679 3086 2.031682 CCTTATATGCTCGTTGGCAAGC 60.032 50.000 0.00 0.39 45.68 4.01
2697 3104 4.813697 GCAAGCGAGGAGAATTTTATCTCT 59.186 41.667 4.50 0.00 44.30 3.10
2915 3322 3.507233 GTGCTGGATCTTGGAAATTGTGA 59.493 43.478 0.00 0.00 0.00 3.58
2942 3349 5.041940 CCGTAAAAGTAGCTCTGGTATCAC 58.958 45.833 0.00 0.00 0.00 3.06
2949 3356 2.551270 AGCTCTGGTATCACCCTCAAA 58.449 47.619 0.00 0.00 37.50 2.69
3089 3496 9.583765 AACTCGTATAGAAGAATTACCTTCAAC 57.416 33.333 8.99 4.34 43.68 3.18
3237 3644 3.701664 TGTGGAAGAGCTGAGTCATCTA 58.298 45.455 0.00 0.00 0.00 1.98
3369 3782 3.018856 TGATGGTGGCAGATTGAATGAC 58.981 45.455 0.00 0.00 0.00 3.06
3376 3789 1.268896 GCAGATTGAATGACCGCATGG 60.269 52.381 0.00 0.00 42.84 3.66
3430 3843 3.352648 AGTTTTGATTCATGGTACCCCG 58.647 45.455 10.07 0.00 0.00 5.73
3450 3866 2.872245 CGCTTCTTCTTTGTGGTTCTCA 59.128 45.455 0.00 0.00 0.00 3.27
3503 3919 2.203998 CCACCTCTCCACCCTGGT 60.204 66.667 0.00 0.00 39.03 4.00
3522 3938 7.162082 CCCTGGTAATATATGTGGAAGAACTC 58.838 42.308 0.00 0.00 0.00 3.01
3553 3969 5.120054 TGACATTCAGATCATTGGGATGT 57.880 39.130 0.00 0.00 36.00 3.06
3638 4054 1.311859 GATGCATTCCCATCTGCGAA 58.688 50.000 0.00 0.00 41.32 4.70
3639 4055 1.266175 GATGCATTCCCATCTGCGAAG 59.734 52.381 0.00 0.00 41.32 3.79
3698 4114 0.991146 TTTCCACCTGGAGCTATGCA 59.009 50.000 0.00 0.00 46.36 3.96
3705 4121 1.673168 CTGGAGCTATGCAAAGGGTC 58.327 55.000 0.00 0.00 0.00 4.46
3715 4131 1.002624 CAAAGGGTCCAGCGCCTTA 60.003 57.895 2.29 0.00 30.80 2.69
3722 4138 0.669625 GTCCAGCGCCTTAAGTTCGT 60.670 55.000 2.29 1.86 0.00 3.85
3743 4159 1.268079 GGTCTCTGCATCATCGATCGA 59.732 52.381 21.86 21.86 0.00 3.59
3753 4169 2.876091 TCATCGATCGAAAGTGGTGAC 58.124 47.619 23.50 0.00 0.00 3.67
3764 4180 2.964925 TGGTGACGTTGACTGCGC 60.965 61.111 0.00 0.00 0.00 6.09
3837 4265 5.033589 AGAATTCCAGCGATGAAGAGATT 57.966 39.130 0.06 0.00 0.00 2.40
3952 4380 1.685765 TGACATACCTCTGCGGCCT 60.686 57.895 0.00 0.00 35.61 5.19
4026 4464 6.781138 TGAAAATGCTCGTTACCATATTGTC 58.219 36.000 0.00 0.00 0.00 3.18
4050 4491 7.650104 GTCTGATTTATCTCTCTTAGTTTCCCG 59.350 40.741 0.00 0.00 0.00 5.14
4102 4576 2.298163 AGGTACTGTTCCAACACTACGG 59.702 50.000 6.23 0.00 37.18 4.02
4103 4577 2.036346 GGTACTGTTCCAACACTACGGT 59.964 50.000 0.00 0.00 32.45 4.83
4104 4578 3.255642 GGTACTGTTCCAACACTACGGTA 59.744 47.826 0.00 0.00 32.45 4.02
4105 4579 4.082026 GGTACTGTTCCAACACTACGGTAT 60.082 45.833 0.00 0.00 36.39 2.73
4129 4603 2.168106 AGGCAACAAACAATTCACTGCA 59.832 40.909 0.00 0.00 41.41 4.41
4180 4654 3.067601 TCATGTGATTCGTGTACGGCTAT 59.932 43.478 4.44 0.00 40.29 2.97
4254 4730 0.109504 GCTAGATAGAGGCTTCCGCG 60.110 60.000 0.00 0.00 36.88 6.46
4257 4733 1.038130 AGATAGAGGCTTCCGCGTGT 61.038 55.000 4.92 0.00 36.88 4.49
4258 4734 0.666913 GATAGAGGCTTCCGCGTGTA 59.333 55.000 4.92 0.00 34.84 2.90
4259 4735 0.384669 ATAGAGGCTTCCGCGTGTAC 59.615 55.000 4.92 0.00 33.46 2.90
4303 4789 2.849880 TTTCCGCATATGCTTTCAGC 57.150 45.000 24.56 0.00 42.82 4.26
4335 4821 4.181051 GGCTGTTCCTGCCTTGTT 57.819 55.556 5.03 0.00 43.62 2.83
4336 4822 3.339547 GGCTGTTCCTGCCTTGTTA 57.660 52.632 5.03 0.00 43.62 2.41
4337 4823 1.839424 GGCTGTTCCTGCCTTGTTAT 58.161 50.000 5.03 0.00 43.62 1.89
4338 4824 2.999331 GGCTGTTCCTGCCTTGTTATA 58.001 47.619 5.03 0.00 43.62 0.98
4424 4910 6.829229 TCTTTATCCAGTCAAGACTCGTAA 57.171 37.500 0.00 0.00 40.20 3.18
4444 4930 9.467258 CTCGTAAAATAATAGGTTACATTCCGA 57.533 33.333 0.00 0.00 0.00 4.55
4445 4931 9.985730 TCGTAAAATAATAGGTTACATTCCGAT 57.014 29.630 0.00 0.00 0.00 4.18
4449 4935 8.617290 AAATAATAGGTTACATTCCGATGTCC 57.383 34.615 0.00 0.00 42.83 4.02
4450 4936 4.618920 ATAGGTTACATTCCGATGTCCC 57.381 45.455 0.00 0.00 42.83 4.46
4451 4937 2.478292 AGGTTACATTCCGATGTCCCT 58.522 47.619 0.00 0.95 42.83 4.20
4452 4938 2.434702 AGGTTACATTCCGATGTCCCTC 59.565 50.000 0.00 0.00 42.83 4.30
4453 4939 2.434702 GGTTACATTCCGATGTCCCTCT 59.565 50.000 0.00 0.00 42.83 3.69
4454 4940 3.118371 GGTTACATTCCGATGTCCCTCTT 60.118 47.826 0.00 0.00 42.83 2.85
4456 4942 2.187958 ACATTCCGATGTCCCTCTTCA 58.812 47.619 0.00 0.00 42.83 3.02
4465 4951 5.590259 CCGATGTCCCTCTTCAATTTGTAAT 59.410 40.000 0.00 0.00 0.00 1.89
4466 4952 6.458751 CCGATGTCCCTCTTCAATTTGTAATG 60.459 42.308 0.00 0.00 0.00 1.90
4471 4957 5.885912 TCCCTCTTCAATTTGTAATGCTACC 59.114 40.000 0.00 0.00 0.00 3.18
4472 4958 5.888161 CCCTCTTCAATTTGTAATGCTACCT 59.112 40.000 0.00 0.00 0.00 3.08
4480 4966 6.808321 ATTTGTAATGCTACCTCCTCTACA 57.192 37.500 0.00 0.00 0.00 2.74
4482 4968 6.808321 TTGTAATGCTACCTCCTCTACATT 57.192 37.500 0.00 0.00 0.00 2.71
4483 4969 6.808321 TGTAATGCTACCTCCTCTACATTT 57.192 37.500 0.00 0.00 0.00 2.32
4485 4971 8.313944 TGTAATGCTACCTCCTCTACATTTTA 57.686 34.615 0.00 0.00 0.00 1.52
4486 4972 8.764558 TGTAATGCTACCTCCTCTACATTTTAA 58.235 33.333 0.00 0.00 0.00 1.52
4487 4973 9.780186 GTAATGCTACCTCCTCTACATTTTAAT 57.220 33.333 0.00 0.00 0.00 1.40
4489 4975 9.700831 AATGCTACCTCCTCTACATTTTAATTT 57.299 29.630 0.00 0.00 0.00 1.82
4490 4976 8.732746 TGCTACCTCCTCTACATTTTAATTTC 57.267 34.615 0.00 0.00 0.00 2.17
4511 4997 8.752766 ATTTCTTCATTTGCTTGTTCACATAG 57.247 30.769 0.00 0.00 0.00 2.23
4513 4999 7.509141 TCTTCATTTGCTTGTTCACATAGAA 57.491 32.000 0.00 0.00 0.00 2.10
4551 5037 9.801873 TTTTATTGGCTTATTAATGAAGAGCAC 57.198 29.630 13.35 6.77 35.12 4.40
4552 5038 5.835113 TTGGCTTATTAATGAAGAGCACC 57.165 39.130 13.35 5.44 35.12 5.01
4554 5040 4.883585 TGGCTTATTAATGAAGAGCACCTG 59.116 41.667 13.35 0.00 35.12 4.00
4599 5267 8.755028 TGTTGTAGCTTCTACTATGATTTACCA 58.245 33.333 6.50 0.00 0.00 3.25
4600 5268 9.250624 GTTGTAGCTTCTACTATGATTTACCAG 57.749 37.037 0.00 0.00 0.00 4.00
4602 5270 8.630917 TGTAGCTTCTACTATGATTTACCAGAC 58.369 37.037 0.00 0.00 0.00 3.51
4603 5271 6.740110 AGCTTCTACTATGATTTACCAGACG 58.260 40.000 0.00 0.00 0.00 4.18
4604 5272 5.921408 GCTTCTACTATGATTTACCAGACGG 59.079 44.000 0.00 0.00 38.77 4.79
4605 5273 6.238953 GCTTCTACTATGATTTACCAGACGGA 60.239 42.308 0.00 0.00 35.59 4.69
4606 5274 6.879276 TCTACTATGATTTACCAGACGGAG 57.121 41.667 0.00 0.00 35.59 4.63
4607 5275 4.939052 ACTATGATTTACCAGACGGAGG 57.061 45.455 0.00 0.00 35.59 4.30
4608 5276 2.622064 ATGATTTACCAGACGGAGGC 57.378 50.000 0.00 0.00 35.59 4.70
4609 5277 1.568504 TGATTTACCAGACGGAGGCT 58.431 50.000 0.00 0.00 35.59 4.58
4610 5278 1.906574 TGATTTACCAGACGGAGGCTT 59.093 47.619 0.00 0.00 35.59 4.35
4613 5281 0.895530 TTACCAGACGGAGGCTTCTG 59.104 55.000 2.55 2.55 39.25 3.02
4614 5282 1.605058 TACCAGACGGAGGCTTCTGC 61.605 60.000 4.24 0.00 38.36 4.26
4615 5283 2.659016 CAGACGGAGGCTTCTGCA 59.341 61.111 4.24 0.00 41.91 4.41
4617 5285 1.088340 CAGACGGAGGCTTCTGCATG 61.088 60.000 4.24 0.00 41.91 4.06
4624 6203 1.881973 GAGGCTTCTGCATGTTGTTCA 59.118 47.619 0.00 0.00 41.91 3.18
4654 6233 3.325870 TGGATTAGTTGTGTTCTCTGCG 58.674 45.455 0.00 0.00 0.00 5.18
4658 6237 5.581085 GGATTAGTTGTGTTCTCTGCGTATT 59.419 40.000 0.00 0.00 0.00 1.89
4681 6260 1.167851 TCAGCAATGCAGTGCCTTAC 58.832 50.000 33.28 8.07 46.14 2.34
4684 6263 2.749076 CAGCAATGCAGTGCCTTACTTA 59.251 45.455 33.28 0.00 46.14 2.24
4699 6278 8.039538 GTGCCTTACTTAGTTCCTAATTGTACT 58.960 37.037 0.00 0.00 0.00 2.73
4713 6292 7.121168 TCCTAATTGTACTGCTTGATTTCCTTG 59.879 37.037 0.00 0.00 0.00 3.61
4714 6293 6.655078 AATTGTACTGCTTGATTTCCTTGT 57.345 33.333 0.00 0.00 0.00 3.16
4716 6295 4.460263 TGTACTGCTTGATTTCCTTGTGT 58.540 39.130 0.00 0.00 0.00 3.72
4726 6305 3.974871 TTTCCTTGTGTCGGCTTTAAC 57.025 42.857 0.00 0.00 0.00 2.01
4753 6332 5.338056 GGACCCCATTTCCTTTTATTCAACC 60.338 44.000 0.00 0.00 0.00 3.77
4754 6333 5.158889 ACCCCATTTCCTTTTATTCAACCA 58.841 37.500 0.00 0.00 0.00 3.67
4757 6336 6.013812 CCCCATTTCCTTTTATTCAACCAAGA 60.014 38.462 0.00 0.00 0.00 3.02
4758 6337 7.099120 CCCATTTCCTTTTATTCAACCAAGAG 58.901 38.462 0.00 0.00 0.00 2.85
4760 6339 6.723298 TTTCCTTTTATTCAACCAAGAGCA 57.277 33.333 0.00 0.00 0.00 4.26
4761 6340 6.723298 TTCCTTTTATTCAACCAAGAGCAA 57.277 33.333 0.00 0.00 0.00 3.91
4762 6341 6.331369 TCCTTTTATTCAACCAAGAGCAAG 57.669 37.500 0.00 0.00 0.00 4.01
4763 6342 6.068010 TCCTTTTATTCAACCAAGAGCAAGA 58.932 36.000 0.00 0.00 0.00 3.02
4765 6344 7.233348 TCCTTTTATTCAACCAAGAGCAAGATT 59.767 33.333 0.00 0.00 0.00 2.40
4766 6345 7.543520 CCTTTTATTCAACCAAGAGCAAGATTC 59.456 37.037 0.00 0.00 0.00 2.52
4767 6346 4.691860 ATTCAACCAAGAGCAAGATTCG 57.308 40.909 0.00 0.00 0.00 3.34
4769 6348 4.265904 TCAACCAAGAGCAAGATTCGTA 57.734 40.909 0.00 0.00 0.00 3.43
4770 6349 4.245660 TCAACCAAGAGCAAGATTCGTAG 58.754 43.478 0.00 0.00 0.00 3.51
4772 6351 5.047590 TCAACCAAGAGCAAGATTCGTAGTA 60.048 40.000 0.00 0.00 0.00 1.82
4773 6352 4.745649 ACCAAGAGCAAGATTCGTAGTAC 58.254 43.478 0.00 0.00 0.00 2.73
4775 6354 5.168569 CCAAGAGCAAGATTCGTAGTACAA 58.831 41.667 0.38 0.00 0.00 2.41
4778 6357 6.208988 AGAGCAAGATTCGTAGTACAATGA 57.791 37.500 0.38 0.00 0.00 2.57
4780 6359 7.097192 AGAGCAAGATTCGTAGTACAATGAAA 58.903 34.615 0.38 0.00 0.00 2.69
4781 6360 7.766278 AGAGCAAGATTCGTAGTACAATGAAAT 59.234 33.333 0.38 0.00 0.00 2.17
4782 6361 7.688372 AGCAAGATTCGTAGTACAATGAAATG 58.312 34.615 0.38 0.00 0.00 2.32
4785 6364 9.265938 CAAGATTCGTAGTACAATGAAATGTTG 57.734 33.333 0.38 0.41 34.75 3.33
4786 6365 7.464358 AGATTCGTAGTACAATGAAATGTTGC 58.536 34.615 0.38 0.00 34.75 4.17
4787 6366 6.546972 TTCGTAGTACAATGAAATGTTGCA 57.453 33.333 0.38 0.00 34.75 4.08
4789 6368 7.139896 TCGTAGTACAATGAAATGTTGCATT 57.860 32.000 0.38 0.00 35.24 3.56
4794 6373 4.392619 CAATGAAATGTTGCATTGCGTT 57.607 36.364 12.25 0.00 43.12 4.84
4795 6374 4.145276 CAATGAAATGTTGCATTGCGTTG 58.855 39.130 16.01 16.01 43.12 4.10
4796 6375 2.819115 TGAAATGTTGCATTGCGTTGT 58.181 38.095 3.84 0.00 0.00 3.32
4797 6376 2.538861 TGAAATGTTGCATTGCGTTGTG 59.461 40.909 3.84 0.00 0.00 3.33
4798 6377 2.222007 AATGTTGCATTGCGTTGTGT 57.778 40.000 3.84 0.00 0.00 3.72
4799 6378 3.361794 AATGTTGCATTGCGTTGTGTA 57.638 38.095 3.84 0.00 0.00 2.90
4800 6379 2.112475 TGTTGCATTGCGTTGTGTAC 57.888 45.000 3.84 0.00 0.00 2.90
4826 6405 0.034089 CCGAGGCCCCTCTTCATTTT 60.034 55.000 12.21 0.00 40.69 1.82
4827 6406 1.098050 CGAGGCCCCTCTTCATTTTG 58.902 55.000 12.21 0.00 40.69 2.44
4829 6408 2.355716 CGAGGCCCCTCTTCATTTTGTA 60.356 50.000 12.21 0.00 40.69 2.41
4830 6409 3.697166 GAGGCCCCTCTTCATTTTGTAA 58.303 45.455 0.00 0.00 39.80 2.41
4831 6410 3.431415 AGGCCCCTCTTCATTTTGTAAC 58.569 45.455 0.00 0.00 0.00 2.50
4832 6411 2.163613 GGCCCCTCTTCATTTTGTAACG 59.836 50.000 0.00 0.00 0.00 3.18
4876 7076 3.475575 TCAGTTGCTTGCTCACATACAA 58.524 40.909 0.00 0.00 0.00 2.41
4878 7078 3.003585 CAGTTGCTTGCTCACATACAACA 59.996 43.478 0.00 0.00 41.20 3.33
4901 7116 7.918643 ACATTGTTTTGTTTTGATTGGCTTAG 58.081 30.769 0.00 0.00 0.00 2.18
4902 7117 5.982465 TGTTTTGTTTTGATTGGCTTAGC 57.018 34.783 0.00 0.00 0.00 3.09
4923 7138 2.229062 CGAAGAGCACCTGAGTAGTTGA 59.771 50.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.001974 GGGATGGGCAAAAGTTGAACC 59.998 52.381 0.00 0.00 0.00 3.62
9 10 1.336795 CGGGATGGGCAAAAGTTGAAC 60.337 52.381 0.00 0.00 0.00 3.18
14 15 0.966179 GTTTCGGGATGGGCAAAAGT 59.034 50.000 0.00 0.00 0.00 2.66
22 23 0.732571 CACAATCGGTTTCGGGATGG 59.267 55.000 0.00 0.00 36.95 3.51
222 326 3.960102 ACTGACCATTTTTCCTCTTTGCA 59.040 39.130 0.00 0.00 0.00 4.08
231 335 3.057946 GCTCTGACCACTGACCATTTTTC 60.058 47.826 0.00 0.00 0.00 2.29
265 372 9.374838 GGAAAAGCATGATCTGATTATTTGTTT 57.625 29.630 0.00 0.00 30.63 2.83
266 373 8.533657 TGGAAAAGCATGATCTGATTATTTGTT 58.466 29.630 0.00 0.00 30.63 2.83
268 375 8.936070 TTGGAAAAGCATGATCTGATTATTTG 57.064 30.769 0.00 0.00 30.63 2.32
269 376 9.374838 GTTTGGAAAAGCATGATCTGATTATTT 57.625 29.630 0.00 0.00 30.63 1.40
270 377 8.533657 TGTTTGGAAAAGCATGATCTGATTATT 58.466 29.630 0.00 0.00 30.63 1.40
271 378 8.070034 TGTTTGGAAAAGCATGATCTGATTAT 57.930 30.769 0.00 0.00 30.63 1.28
272 379 7.465353 TGTTTGGAAAAGCATGATCTGATTA 57.535 32.000 0.00 0.00 30.63 1.75
273 380 6.349243 TGTTTGGAAAAGCATGATCTGATT 57.651 33.333 0.00 0.00 34.16 2.57
274 381 5.988310 TGTTTGGAAAAGCATGATCTGAT 57.012 34.783 0.00 0.00 0.00 2.90
276 383 7.429636 AATTTGTTTGGAAAAGCATGATCTG 57.570 32.000 0.00 0.00 0.00 2.90
277 384 8.370182 ACTAATTTGTTTGGAAAAGCATGATCT 58.630 29.630 0.00 0.00 0.00 2.75
281 388 6.705381 TCCACTAATTTGTTTGGAAAAGCATG 59.295 34.615 0.00 0.00 35.13 4.06
282 389 6.825610 TCCACTAATTTGTTTGGAAAAGCAT 58.174 32.000 0.00 0.00 35.13 3.79
286 393 9.362151 AGATACTCCACTAATTTGTTTGGAAAA 57.638 29.630 1.94 0.00 37.69 2.29
293 400 9.349713 TGTTTTCAGATACTCCACTAATTTGTT 57.650 29.630 0.00 0.00 0.00 2.83
294 401 8.918202 TGTTTTCAGATACTCCACTAATTTGT 57.082 30.769 0.00 0.00 0.00 2.83
295 402 9.612620 GTTGTTTTCAGATACTCCACTAATTTG 57.387 33.333 0.00 0.00 0.00 2.32
296 403 9.574516 AGTTGTTTTCAGATACTCCACTAATTT 57.425 29.630 0.00 0.00 0.00 1.82
298 405 9.877178 CTAGTTGTTTTCAGATACTCCACTAAT 57.123 33.333 0.00 0.00 0.00 1.73
301 408 7.304497 ACTAGTTGTTTTCAGATACTCCACT 57.696 36.000 0.00 0.00 0.00 4.00
302 409 9.088512 CATACTAGTTGTTTTCAGATACTCCAC 57.911 37.037 0.00 0.00 0.00 4.02
303 410 7.764443 GCATACTAGTTGTTTTCAGATACTCCA 59.236 37.037 0.00 0.00 0.00 3.86
304 411 7.224949 GGCATACTAGTTGTTTTCAGATACTCC 59.775 40.741 0.00 0.00 0.00 3.85
305 412 7.224949 GGGCATACTAGTTGTTTTCAGATACTC 59.775 40.741 0.00 0.00 0.00 2.59
306 413 7.048512 GGGCATACTAGTTGTTTTCAGATACT 58.951 38.462 0.00 0.00 0.00 2.12
307 414 6.018994 CGGGCATACTAGTTGTTTTCAGATAC 60.019 42.308 0.00 0.00 0.00 2.24
309 416 4.876107 CGGGCATACTAGTTGTTTTCAGAT 59.124 41.667 0.00 0.00 0.00 2.90
312 419 3.244630 ACCGGGCATACTAGTTGTTTTCA 60.245 43.478 6.32 0.00 0.00 2.69
313 420 3.340928 ACCGGGCATACTAGTTGTTTTC 58.659 45.455 6.32 0.00 0.00 2.29
314 421 3.428413 ACCGGGCATACTAGTTGTTTT 57.572 42.857 6.32 0.00 0.00 2.43
315 422 3.428413 AACCGGGCATACTAGTTGTTT 57.572 42.857 6.32 0.00 0.00 2.83
316 423 3.428413 AAACCGGGCATACTAGTTGTT 57.572 42.857 6.32 0.00 0.00 2.83
317 424 3.428413 AAAACCGGGCATACTAGTTGT 57.572 42.857 6.32 0.00 0.00 3.32
318 425 3.128068 GGAAAAACCGGGCATACTAGTTG 59.872 47.826 6.32 0.52 0.00 3.16
319 426 3.244981 TGGAAAAACCGGGCATACTAGTT 60.245 43.478 6.32 0.00 42.61 2.24
320 427 2.306512 TGGAAAAACCGGGCATACTAGT 59.693 45.455 6.32 0.00 42.61 2.57
322 429 3.436577 TTGGAAAAACCGGGCATACTA 57.563 42.857 6.32 0.00 42.61 1.82
324 431 2.036089 TGTTTGGAAAAACCGGGCATAC 59.964 45.455 6.32 0.00 42.61 2.39
325 432 2.317040 TGTTTGGAAAAACCGGGCATA 58.683 42.857 6.32 0.00 42.61 3.14
327 434 0.902531 TTGTTTGGAAAAACCGGGCA 59.097 45.000 6.32 0.00 42.61 5.36
328 435 2.025589 TTTGTTTGGAAAAACCGGGC 57.974 45.000 6.32 0.00 42.61 6.13
334 441 6.038050 GCATGATCTGGTTTTGTTTGGAAAAA 59.962 34.615 0.00 0.00 0.00 1.94
336 443 5.055812 GCATGATCTGGTTTTGTTTGGAAA 58.944 37.500 0.00 0.00 0.00 3.13
337 444 4.344679 AGCATGATCTGGTTTTGTTTGGAA 59.655 37.500 0.00 0.00 29.07 3.53
349 510 4.524316 TGTTTGGAAAAGCATGATCTGG 57.476 40.909 0.00 0.00 0.00 3.86
413 574 1.227999 CGGACGAGCAAAAGCTGGAA 61.228 55.000 6.49 0.00 0.00 3.53
428 589 2.224113 TGTTTACAGAGAACCACCGGAC 60.224 50.000 9.46 0.00 0.00 4.79
444 605 6.600032 TCAGCAAAAACCAGACTAACTGTTTA 59.400 34.615 0.00 0.00 44.40 2.01
456 619 3.855689 ATCCGATTCAGCAAAAACCAG 57.144 42.857 0.00 0.00 0.00 4.00
470 636 9.671279 TCTGCACATAATAAATTCATATCCGAT 57.329 29.630 0.00 0.00 0.00 4.18
506 680 4.020128 ACCCAAGATGAACTAGTGGAGAAC 60.020 45.833 0.00 0.00 30.33 3.01
581 777 0.956633 CCAAAGCAGAAGCAGAAGCA 59.043 50.000 0.00 0.00 45.49 3.91
582 778 1.242076 TCCAAAGCAGAAGCAGAAGC 58.758 50.000 0.00 0.00 45.49 3.86
631 833 2.955660 TGATTGGTTGGTGAAAGTGACC 59.044 45.455 0.00 0.00 0.00 4.02
692 894 4.553429 GGTCGAAATTCTGTAATGCAAACG 59.447 41.667 0.00 0.00 0.00 3.60
834 1043 5.011738 TCGTTTCTCCAGGTTGTATTCTCTT 59.988 40.000 0.00 0.00 0.00 2.85
888 1097 1.524848 CATGCATCATCTCCAGCTCC 58.475 55.000 0.00 0.00 0.00 4.70
968 1177 1.537397 TCTCTCACCTTGCCAGCCT 60.537 57.895 0.00 0.00 0.00 4.58
1056 1265 2.002586 CGATTCTTCATGCTCGTTGGT 58.997 47.619 0.00 0.00 0.00 3.67
1064 1273 4.629200 ACTTCTTGACTCGATTCTTCATGC 59.371 41.667 4.29 0.00 0.00 4.06
1070 1279 6.090483 TGAGAAACTTCTTGACTCGATTCT 57.910 37.500 4.29 0.00 37.73 2.40
1160 1369 3.795688 ACTCCTTGGCAAGATCTTGAA 57.204 42.857 34.43 20.97 42.93 2.69
1232 1441 0.981183 ACGAGGGTCAATGGTAGCAA 59.019 50.000 0.00 0.00 0.00 3.91
1364 1573 5.243730 CCACCAACACCAACAATAGAGATTT 59.756 40.000 0.00 0.00 0.00 2.17
1476 1685 9.532494 TCTTTGAAATTTTTCCTGATATCTGGA 57.468 29.630 23.44 23.44 41.40 3.86
1492 1701 6.069381 AGGCCATAGAGTAGGTCTTTGAAATT 60.069 38.462 5.01 0.00 36.13 1.82
1493 1702 5.430089 AGGCCATAGAGTAGGTCTTTGAAAT 59.570 40.000 5.01 0.00 36.13 2.17
1810 2194 7.647907 AAAATGTTAAGAAATGCAGCAGAAG 57.352 32.000 0.00 0.00 0.00 2.85
1854 2238 5.079643 AGCAAACCACAGGAATTATTCAGT 58.920 37.500 7.29 2.22 0.00 3.41
1855 2239 5.649782 AGCAAACCACAGGAATTATTCAG 57.350 39.130 7.29 1.60 0.00 3.02
1888 2290 8.976986 ACTGAATCTTGCAACAAAGATAATTC 57.023 30.769 0.00 0.00 44.35 2.17
1923 2329 8.856153 TTAGTATCATAAGTTGGCAAGTCAAA 57.144 30.769 8.24 0.00 0.00 2.69
2019 2426 3.305897 GGAGTTTGTTTTTCCACAAAGCG 59.694 43.478 0.00 0.00 45.23 4.68
2028 2435 4.517832 ACCCGACTATGGAGTTTGTTTTTC 59.482 41.667 0.00 0.00 35.45 2.29
2194 2601 0.899720 ACTACCCGCAAATCTTCCGA 59.100 50.000 0.00 0.00 0.00 4.55
2196 2603 3.057734 CGATACTACCCGCAAATCTTCC 58.942 50.000 0.00 0.00 0.00 3.46
2219 2626 9.304731 CACCACCACATTTCTTCAATATATTTG 57.695 33.333 0.00 0.00 0.00 2.32
2221 2628 8.593945 ACACCACCACATTTCTTCAATATATT 57.406 30.769 0.00 0.00 0.00 1.28
2274 2681 1.351017 CTTTGGCCACTAACCAGGAGA 59.649 52.381 3.88 0.00 38.73 3.71
2287 2694 4.893608 TCTTTTTGCTTTATCCTTTGGCC 58.106 39.130 0.00 0.00 0.00 5.36
2333 2740 1.195442 TGTAACTCCACGGCCCATCA 61.195 55.000 0.00 0.00 0.00 3.07
2355 2762 2.871096 TGTCCTTCACAATACCACCC 57.129 50.000 0.00 0.00 29.30 4.61
2406 2813 4.508461 TGTCTTCAAATGTGATGGCAAG 57.492 40.909 3.67 0.00 39.73 4.01
2471 2878 5.887598 CACCTCCATATCAACCAATCTTTCA 59.112 40.000 0.00 0.00 0.00 2.69
2474 2881 4.796606 CCACCTCCATATCAACCAATCTT 58.203 43.478 0.00 0.00 0.00 2.40
2547 2954 3.181495 CGTTGAAGTAGCTCTCTCCGATT 60.181 47.826 0.00 0.00 0.00 3.34
2592 2999 2.938451 CTCGTTGATATTTGCTGGCTGA 59.062 45.455 0.00 0.00 0.00 4.26
2604 3011 2.173519 ACCGTTCCTTCCTCGTTGATA 58.826 47.619 0.00 0.00 0.00 2.15
2626 3033 5.700832 CCATATCATGTATACGGCAAGTTGT 59.299 40.000 4.48 0.00 0.00 3.32
2627 3034 5.700832 ACCATATCATGTATACGGCAAGTTG 59.299 40.000 0.00 0.00 25.41 3.16
2674 3081 4.813697 AGAGATAAAATTCTCCTCGCTTGC 59.186 41.667 0.00 0.00 42.63 4.01
2697 3104 6.125589 TGCCACTCAGCATTATCCAATATA 57.874 37.500 0.00 0.00 38.00 0.86
2915 3322 2.353803 CCAGAGCTACTTTTACGGCTGT 60.354 50.000 2.42 2.42 35.01 4.40
3134 3541 2.629656 CCTTTTGGCAGCCTCACCG 61.630 63.158 14.15 0.00 0.00 4.94
3237 3644 3.322254 CACTGAGTGTCCTAACCTCTGTT 59.678 47.826 4.01 0.00 35.12 3.16
3369 3782 2.513204 CAGCTCTCACCCATGCGG 60.513 66.667 0.00 0.00 37.81 5.69
3430 3843 3.303395 CGTGAGAACCACAAAGAAGAAGC 60.303 47.826 0.00 0.00 45.98 3.86
3450 3866 3.564053 TTAACCCACTTTGGAAGTCGT 57.436 42.857 0.00 0.00 40.96 4.34
3522 3938 3.117776 TGATCTGAATGTCATCCCCTTGG 60.118 47.826 0.00 0.00 0.00 3.61
3553 3969 0.108585 AGAAACCGAAGAGCAGGCAA 59.891 50.000 0.00 0.00 0.00 4.52
3638 4054 0.322277 CCCTCTGAACATGCAGCACT 60.322 55.000 0.00 0.00 35.86 4.40
3639 4055 0.607489 ACCCTCTGAACATGCAGCAC 60.607 55.000 0.00 0.00 35.86 4.40
3698 4114 0.322546 CTTAAGGCGCTGGACCCTTT 60.323 55.000 7.64 0.00 41.49 3.11
3705 4121 1.635663 CCACGAACTTAAGGCGCTGG 61.636 60.000 7.64 17.30 0.00 4.85
3715 4131 1.344438 TGATGCAGAGACCACGAACTT 59.656 47.619 0.00 0.00 0.00 2.66
3722 4138 1.000938 CGATCGATGATGCAGAGACCA 60.001 52.381 10.26 0.00 0.00 4.02
3743 4159 1.014352 GCAGTCAACGTCACCACTTT 58.986 50.000 0.00 0.00 0.00 2.66
3837 4265 1.073722 CCAAGCCTTGGCTGTCTCA 59.926 57.895 15.52 0.00 45.17 3.27
3952 4380 3.585289 TGATTAGACCTTACCAGTGGCAA 59.415 43.478 9.78 0.78 0.00 4.52
4026 4464 6.926272 CCGGGAAACTAAGAGAGATAAATCAG 59.074 42.308 0.00 0.00 0.00 2.90
4050 4491 4.498241 GATTTCATTGAAGGCCTGAAACC 58.502 43.478 16.74 6.19 40.54 3.27
4102 4576 7.432252 GCAGTGAATTGTTTGTTGCCTATATAC 59.568 37.037 0.00 0.00 0.00 1.47
4103 4577 7.121907 TGCAGTGAATTGTTTGTTGCCTATATA 59.878 33.333 0.00 0.00 0.00 0.86
4104 4578 6.071447 TGCAGTGAATTGTTTGTTGCCTATAT 60.071 34.615 0.00 0.00 0.00 0.86
4105 4579 5.242615 TGCAGTGAATTGTTTGTTGCCTATA 59.757 36.000 0.00 0.00 0.00 1.31
4180 4654 2.102588 GAGCCCTCGTTATTTGGAGCTA 59.897 50.000 0.00 0.00 31.14 3.32
4254 4730 7.692088 ACTAGTACATCATGAACTACGTACAC 58.308 38.462 17.51 3.29 33.35 2.90
4303 4789 1.746615 AGCCTGCGGTACTGCATTG 60.747 57.895 28.86 22.47 45.26 2.82
4336 4822 9.765795 GCAGTGACAATAAGTAAGGAACTATAT 57.234 33.333 0.00 0.00 38.49 0.86
4337 4823 8.978472 AGCAGTGACAATAAGTAAGGAACTATA 58.022 33.333 0.00 0.00 38.49 1.31
4338 4824 7.852263 AGCAGTGACAATAAGTAAGGAACTAT 58.148 34.615 0.00 0.00 38.49 2.12
4424 4910 7.664318 GGGACATCGGAATGTAACCTATTATTT 59.336 37.037 5.12 0.00 46.20 1.40
4442 4928 6.489675 CATTACAAATTGAAGAGGGACATCG 58.510 40.000 0.00 0.00 0.00 3.84
4444 4930 5.954150 AGCATTACAAATTGAAGAGGGACAT 59.046 36.000 0.00 0.00 0.00 3.06
4445 4931 5.324409 AGCATTACAAATTGAAGAGGGACA 58.676 37.500 0.00 0.00 0.00 4.02
4447 4933 5.885912 GGTAGCATTACAAATTGAAGAGGGA 59.114 40.000 0.00 0.00 0.00 4.20
4448 4934 5.888161 AGGTAGCATTACAAATTGAAGAGGG 59.112 40.000 0.00 0.00 0.00 4.30
4449 4935 6.038714 GGAGGTAGCATTACAAATTGAAGAGG 59.961 42.308 0.00 0.00 0.00 3.69
4450 4936 6.825721 AGGAGGTAGCATTACAAATTGAAGAG 59.174 38.462 0.00 0.00 0.00 2.85
4451 4937 6.721318 AGGAGGTAGCATTACAAATTGAAGA 58.279 36.000 0.00 0.00 0.00 2.87
4452 4938 6.825721 AGAGGAGGTAGCATTACAAATTGAAG 59.174 38.462 0.00 0.00 0.00 3.02
4453 4939 6.721318 AGAGGAGGTAGCATTACAAATTGAA 58.279 36.000 0.00 0.00 0.00 2.69
4454 4940 6.313519 AGAGGAGGTAGCATTACAAATTGA 57.686 37.500 0.00 0.00 0.00 2.57
4456 4942 7.195374 TGTAGAGGAGGTAGCATTACAAATT 57.805 36.000 0.00 0.00 0.00 1.82
4465 4951 8.548877 AGAAATTAAAATGTAGAGGAGGTAGCA 58.451 33.333 0.00 0.00 0.00 3.49
4466 4952 8.966069 AGAAATTAAAATGTAGAGGAGGTAGC 57.034 34.615 0.00 0.00 0.00 3.58
4482 4968 9.376075 TGTGAACAAGCAAATGAAGAAATTAAA 57.624 25.926 0.00 0.00 0.00 1.52
4483 4969 8.939201 TGTGAACAAGCAAATGAAGAAATTAA 57.061 26.923 0.00 0.00 0.00 1.40
4485 4971 9.199982 CTATGTGAACAAGCAAATGAAGAAATT 57.800 29.630 0.00 0.00 0.00 1.82
4486 4972 8.579006 TCTATGTGAACAAGCAAATGAAGAAAT 58.421 29.630 0.00 0.00 0.00 2.17
4487 4973 7.939782 TCTATGTGAACAAGCAAATGAAGAAA 58.060 30.769 0.00 0.00 0.00 2.52
4488 4974 7.509141 TCTATGTGAACAAGCAAATGAAGAA 57.491 32.000 0.00 0.00 0.00 2.52
4489 4975 7.509141 TTCTATGTGAACAAGCAAATGAAGA 57.491 32.000 0.00 0.00 0.00 2.87
4511 4997 8.587952 AAGCCAATAAAAACATAACACTGTTC 57.412 30.769 0.00 0.00 38.38 3.18
4527 5013 7.779798 AGGTGCTCTTCATTAATAAGCCAATAA 59.220 33.333 8.13 0.00 31.96 1.40
4530 5016 5.357878 CAGGTGCTCTTCATTAATAAGCCAA 59.642 40.000 8.13 0.00 31.96 4.52
4543 5029 1.339151 CCAACTACCCAGGTGCTCTTC 60.339 57.143 0.00 0.00 38.24 2.87
4549 5035 2.227194 GTTGAACCAACTACCCAGGTG 58.773 52.381 0.00 0.00 40.73 4.00
4550 5036 2.651382 GTTGAACCAACTACCCAGGT 57.349 50.000 2.85 0.00 40.73 4.00
4583 5251 5.768662 CCTCCGTCTGGTAAATCATAGTAGA 59.231 44.000 0.00 0.00 36.30 2.59
4585 5253 4.280174 GCCTCCGTCTGGTAAATCATAGTA 59.720 45.833 0.00 0.00 36.30 1.82
4586 5254 3.069729 GCCTCCGTCTGGTAAATCATAGT 59.930 47.826 0.00 0.00 36.30 2.12
4587 5255 3.322254 AGCCTCCGTCTGGTAAATCATAG 59.678 47.826 0.00 0.00 36.30 2.23
4589 5257 2.119495 AGCCTCCGTCTGGTAAATCAT 58.881 47.619 0.00 0.00 36.30 2.45
4592 5260 2.093447 CAGAAGCCTCCGTCTGGTAAAT 60.093 50.000 0.00 0.00 41.85 1.40
4595 5263 1.605058 GCAGAAGCCTCCGTCTGGTA 61.605 60.000 8.32 0.00 44.50 3.25
4597 5265 2.125350 GCAGAAGCCTCCGTCTGG 60.125 66.667 8.32 0.00 44.50 3.86
4599 5267 1.220206 CATGCAGAAGCCTCCGTCT 59.780 57.895 0.00 0.00 41.13 4.18
4600 5268 0.674895 AACATGCAGAAGCCTCCGTC 60.675 55.000 0.00 0.00 41.13 4.79
4602 5270 0.957395 ACAACATGCAGAAGCCTCCG 60.957 55.000 0.00 0.00 41.13 4.63
4603 5271 1.200948 GAACAACATGCAGAAGCCTCC 59.799 52.381 0.00 0.00 41.13 4.30
4604 5272 1.881973 TGAACAACATGCAGAAGCCTC 59.118 47.619 0.00 0.00 41.13 4.70
4605 5273 1.985473 TGAACAACATGCAGAAGCCT 58.015 45.000 0.00 0.00 41.13 4.58
4624 6203 7.170965 AGAACACAACTAATCCAGTTCATCAT 58.829 34.615 0.00 0.00 44.48 2.45
4637 6216 5.779922 AGAATACGCAGAGAACACAACTAA 58.220 37.500 0.00 0.00 0.00 2.24
4645 6224 3.679980 TGCTGAAAGAATACGCAGAGAAC 59.320 43.478 0.00 0.00 34.07 3.01
4654 6233 3.855950 GCACTGCATTGCTGAAAGAATAC 59.144 43.478 20.72 0.00 39.59 1.89
4658 6237 0.599558 GGCACTGCATTGCTGAAAGA 59.400 50.000 25.78 0.00 42.56 2.52
4684 6263 7.121315 GGAAATCAAGCAGTACAATTAGGAACT 59.879 37.037 0.00 0.00 46.37 3.01
4699 6278 1.879380 CCGACACAAGGAAATCAAGCA 59.121 47.619 0.00 0.00 0.00 3.91
4713 6292 2.614779 GGTCCTAGTTAAAGCCGACAC 58.385 52.381 0.00 0.00 0.00 3.67
4714 6293 1.551883 GGGTCCTAGTTAAAGCCGACA 59.448 52.381 0.00 0.00 0.00 4.35
4716 6295 1.197812 GGGGTCCTAGTTAAAGCCGA 58.802 55.000 0.00 0.00 0.00 5.54
4726 6305 6.431722 TGAATAAAAGGAAATGGGGTCCTAG 58.568 40.000 0.00 0.00 45.12 3.02
4753 6332 6.531594 TCATTGTACTACGAATCTTGCTCTTG 59.468 38.462 0.00 0.00 0.00 3.02
4754 6333 6.631016 TCATTGTACTACGAATCTTGCTCTT 58.369 36.000 0.00 0.00 0.00 2.85
4757 6336 7.334421 ACATTTCATTGTACTACGAATCTTGCT 59.666 33.333 0.00 0.00 0.00 3.91
4758 6337 7.464358 ACATTTCATTGTACTACGAATCTTGC 58.536 34.615 0.00 0.00 0.00 4.01
4760 6339 7.962918 GCAACATTTCATTGTACTACGAATCTT 59.037 33.333 0.00 0.00 0.00 2.40
4761 6340 7.119116 TGCAACATTTCATTGTACTACGAATCT 59.881 33.333 0.00 0.00 0.00 2.40
4762 6341 7.240674 TGCAACATTTCATTGTACTACGAATC 58.759 34.615 0.00 0.00 0.00 2.52
4763 6342 7.139896 TGCAACATTTCATTGTACTACGAAT 57.860 32.000 0.00 0.00 0.00 3.34
4765 6344 6.735678 ATGCAACATTTCATTGTACTACGA 57.264 33.333 0.00 0.00 0.00 3.43
4766 6345 6.237279 GCAATGCAACATTTCATTGTACTACG 60.237 38.462 15.30 0.00 46.71 3.51
4767 6346 6.237279 CGCAATGCAACATTTCATTGTACTAC 60.237 38.462 15.30 1.97 46.71 2.73
4769 6348 4.622313 CGCAATGCAACATTTCATTGTACT 59.378 37.500 15.30 0.00 46.71 2.73
4770 6349 4.385447 ACGCAATGCAACATTTCATTGTAC 59.615 37.500 15.30 3.05 46.71 2.90
4772 6351 3.391965 ACGCAATGCAACATTTCATTGT 58.608 36.364 15.30 0.00 46.71 2.71
4775 6354 3.184783 CACAACGCAATGCAACATTTCAT 59.815 39.130 5.91 0.00 0.00 2.57
4778 6357 2.548875 ACACAACGCAATGCAACATTT 58.451 38.095 5.91 0.00 0.00 2.32
4780 6359 2.660490 GTACACAACGCAATGCAACAT 58.340 42.857 5.91 0.00 0.00 2.71
4781 6360 1.595732 CGTACACAACGCAATGCAACA 60.596 47.619 5.91 0.00 46.10 3.33
4782 6361 1.041726 CGTACACAACGCAATGCAAC 58.958 50.000 5.91 0.00 46.10 4.17
4801 6380 1.054978 AAGAGGGGCCTCGGAATACC 61.055 60.000 0.84 0.00 46.90 2.73
4802 6381 0.393448 GAAGAGGGGCCTCGGAATAC 59.607 60.000 0.84 0.00 46.90 1.89
4808 6387 1.098050 CAAAATGAAGAGGGGCCTCG 58.902 55.000 0.84 0.00 46.90 4.63
4831 6410 5.759963 AGAGATTATAACGTAGAGGCAACG 58.240 41.667 5.66 5.66 45.64 4.10
4832 6411 7.201145 TGAAGAGATTATAACGTAGAGGCAAC 58.799 38.462 0.00 0.00 0.00 4.17
4876 7076 6.756299 AAGCCAATCAAAACAAAACAATGT 57.244 29.167 0.00 0.00 34.24 2.71
4878 7078 6.292811 CGCTAAGCCAATCAAAACAAAACAAT 60.293 34.615 0.00 0.00 0.00 2.71
4901 7116 0.528470 ACTACTCAGGTGCTCTTCGC 59.472 55.000 0.00 0.00 39.77 4.70
4902 7117 2.229062 TCAACTACTCAGGTGCTCTTCG 59.771 50.000 0.00 0.00 39.53 3.79


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.